getGenome {regioneR} | R Documentation

## getGenome

### Description

Function to obtain a genome

### Usage

    getGenome(genome)

### Arguments

`genome` | The genome object or genome identifier.

### Details

If genome is a `BSgenome` (from the package `BioStrings`), it will transform it into a `GRanges` with chromosomes and chromosome lengths.

If genome is a `data.frame` with 3 columns, it will transform it into a GRanges.

If genome is a `data.frame` with 2 columns, it will assume the first is the chromosome, the second is the length of the chromosomes and will add 1 as start.

If genome is a `character` string uniquely identifying a `BSgenome` installed in the system (e.g. "hg19", "mm10",... but not "hg"), it will create a genome based on the `BSgenome` object identified by the character string.

If genome is a `GRanges` object, it will return it as is.

If genome is non of the above, it will give a warning and try to transform it into a GRanges using toGRanges. This can be helpful if `genome` is a connection to a file.

### Value

A GRanges object with the "genome" data c(Chromosome, Start (by default, 1), Chromosome Length) given a `BSgenome`, a genome name, a `data.frame` or a GRanges.

A `GRanges` representing the genome with one region per chromosome.

### Note

This function is memoised (cached) using the `memoise` package. To empty the cache, use `forget(getGenome)`

Please note that passing this function the path to a file will not work, since it will assume the character is the identifier of a genome. To read the genome from a file, please use `getGenome(toGRanges("path/to/file"))`

### See Also

`getMask`, `getGenomeAndMask`, `characterToBSGenome`, `maskFromBSGenome`, `emptyCacheRegioneR`

### Examples

    getGenome("hg19")

    getGenome(data.frame(c("chrA", "chrB"), c(15000000, 10000000)))

[Package regioneR version 1.19.2 Index]